Protein receptors are known normally to bind to their target ligands via epitopes, combinations of amino acids, which constitute a small proportion of the total protein molecule.
Protein receptors on the surface of cells are often triggered to produce a signal within the cell as a result of binding to other proteins, termed protein ligands. The portion of the ligand which interacts with the receptor is termed an epitope, and usually constitutes a combination of a small number of amino acids in close proximity with each other, held on the backbone of the peptide chain. Examples of epitopes are those structures on the surface of proteins which interact with antibodies or T-cell receptors, but in fact any structure on the surface of a protein which is recognised specifically by another can fall within the definition of an epitope. Because the binding of a protein receptor with an epitope can be an important step in the etiology of a disease, or conversely, in the treatment of a disease condition, the identification of functional groups which form epitopes is a potentially fruitful avenue for development of new drugs, where the drug is an agent comprising an epitope which binds to the receptor.
Two challenges exist which hinder this approach to new drug development. One is the identification of epitopes which can be employed as drug molecules to bind to appropriate receptors in order to treat a disease. The second challenge is to design molecules which can hold and present the combination of amino acids forming the epitope such that a strong binding interaction with a cell receptor can be achieved.
Methods are known for identifying combination of amino acids which can form epitopes. In traditional combinatorial chemistry, the identification of the most favourable sequence for binding to a specific receptor must be carried out by synthesis of hundreds of possible combinations of different groups such as amino acids, in different orders, each one having to be tested for efficacy. This process is time-consuming, expensive and is limited by the nature of the chemistry which can be carried out in linking the different components together.
WO 01/01140 provides an improved way of identifying epitopes. A composition is provided for interacting with a ligand. The composition comprises a non-covalent assembly of a plurality of distinct conjugates each conjugate comprising a head group and a tail group. The tail groups of the conjugates form a hydrophobic aggregation and the conjugates have freedom of motion with respect to each other within the assembly so that, in the presence of a ligand, at least two of the head groups are appropriately positioned to form an epitope capable of interacting with the ligand more strongly than each of the head groups individually. The plurality of conjugates which has the desired biological activity may be identified by selecting a set of conjugates with an array of head groups, forming a non-covalent association therefrom, in which the tail groups aggregate hydrophobically and in which the conjugates exhibit freedom of motion with respect to one another and assaying for sufficient interaction between the non-covalent association and the ligand. This process may be repeated with a modified array of head groups in order to find sufficient interaction between the non-covalent association and the ligand. This process allows for the identification of the most favourable sequence for binding to a specific receptor by relying on the proximity of the head groups to provide association-derived epitopes without the need for the synthesis of hundreds of possible combinations of different groups using traditional combinatorial chemistry. The method simply relies upon proximity of the head groups to provide association-derived epitopes. Once a set of conjugates has been synthesised, no further synthetic chemistry is required, only simple mixing of the conjugates to form the different probes by non-covalent association.
Whilst this new composition and method have been successful for identifying the functional groups which form the epitope and bind to the target ligand, there is still a requirement to provide improved compositions which are capable of forming the desired epitope and interacting with improved stability and specificity with the target ligand to produce a biological response.
Attempts to produce an analogous peptide to the epitope constructed solely of the amino acids comprising the binding site often fail because these peptides do not possess the same biological activity as the protein receptor.
Where the binding site of a protein is constructed of oligo-peptides from different, non-contiguous parts of a protein chain, attempts to reconstruct the binding site by mixing isolated oligopeptides in free solution does not result in the active binding site.
Accordingly, the present invention aims to provide improved oligopeptides which are capable of forming a desired epitope, which can interact with improved stability and specificity with the target ligand to produce a biological response.